Starting phenix.real_space_refine
on Sun Aug 24 05:52:46 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8ud4_42146/08_2025/8ud4_42146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud4_42146/08_2025/8ud4_42146.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ud4_42146/08_2025/8ud4_42146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud4_42146/08_2025/8ud4_42146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud4_42146/08_2025/8ud4_42146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud4_42146/08_2025/8ud4_42146.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      46      5.49       5
     S      60      5.16       5
     C   11057      2.51       5
     N    2851      2.21       5
     O    3484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17498
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "F"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "D"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "E"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "B"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "A"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "C"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
    Chain: "G"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 463
          Classifications: {'RNA': 23}
          Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 22}
          Link IDs: {'rna3p': 22}
    Chain: "H"
      Number of atoms: 505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 505
          Classifications: {'RNA': 23}
          Modifications used: {'rna3p_pur': 22, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 22}
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N  AILE F  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE F  27 " occ=0.48
    residue:
      pdb=" N  AASN F  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  28 " occ=0.48
    residue:
      pdb=" N  AASN F  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN F  29 " occ=0.48
    residue:
      pdb=" N  AILE D  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE D  27 " occ=0.48
    residue:
      pdb=" N  AASN D  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  28 " occ=0.48
    residue:
      pdb=" N  AASN D  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  29 " occ=0.48
    residue:
      pdb=" N  AILE E  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE E  27 " occ=0.48
    residue:
      pdb=" N  AASN E  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  28 " occ=0.48
    residue:
      pdb=" N  AASN E  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN E  29 " occ=0.48
    residue:
      pdb=" N  AILE B  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE B  27 " occ=0.48
    residue:
      pdb=" N  AASN B  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  28 " occ=0.48
    residue:
      pdb=" N  AASN B  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  29 " occ=0.48
    ... (remaining 6 not shown)
  Time building chain proxies: 6.35, per 1000 atoms: 0.36
  Number of scatterers: 17498
  At special positions: 0
  Unit cell: (115.92, 123.28, 135.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P      46     15.00
     O    3484      8.00
     N    2851      7.00
     C   11057      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.19
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3924

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 44 sheets defined
      26.2% alpha, 23.0% beta
      21 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'F' and resid 1 through 13
    Processing helix  chain 'F' and resid 50 through 60
    Processing helix  chain 'F' and resid 68 through 75
    Processing helix  chain 'F' and resid 113 through 117
    Processing helix  chain 'F' and resid 129 through 137
    Processing helix  chain 'F' and resid 207 through 216
    Processing helix  chain 'F' and resid 217 through 225
    Processing helix  chain 'F' and resid 231 through 236
    Processing helix  chain 'F' and resid 250 through 261
      removed outlier: 3.651A  pdb=" N   GLU F 260 " --> pdb=" O   LYS F 256 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 308
    Processing helix  chain 'D' and resid 2 through 13
    Processing helix  chain 'D' and resid 50 through 60
    Processing helix  chain 'D' and resid 68 through 75
    Processing helix  chain 'D' and resid 129 through 137
    Processing helix  chain 'D' and resid 207 through 216
    Processing helix  chain 'D' and resid 217 through 225
    Processing helix  chain 'D' and resid 231 through 236
    Processing helix  chain 'D' and resid 250 through 261
      removed outlier: 3.585A  pdb=" N   GLU D 260 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 308
    Processing helix  chain 'E' and resid 2 through 13
    Processing helix  chain 'E' and resid 50 through 60
    Processing helix  chain 'E' and resid 68 through 75
    Processing helix  chain 'E' and resid 113 through 117
    Processing helix  chain 'E' and resid 129 through 136
    Processing helix  chain 'E' and resid 207 through 216
    Processing helix  chain 'E' and resid 217 through 226
      removed outlier: 3.566A  pdb=" N   PHE E 221 " --> pdb=" O   ALA E 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 231 through 236
      removed outlier: 3.660A  pdb=" N   VAL E 236 " --> pdb=" O   PHE E 232 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 261
      removed outlier: 3.535A  pdb=" N   GLU E 260 " --> pdb=" O   LYS E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 308
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 50 through 60
    Processing helix  chain 'B' and resid 68 through 75
    Processing helix  chain 'B' and resid 129 through 137
      removed outlier: 3.596A  pdb=" N   LEU B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 216
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.584A  pdb=" N   VAL B 236 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.584A  pdb=" N   GLU B 260 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 308
    Processing helix  chain 'A' and resid 2 through 13
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 129 through 137
    Processing helix  chain 'A' and resid 207 through 216
    Processing helix  chain 'A' and resid 217 through 225
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.681A  pdb=" N   VAL A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.665A  pdb=" N   GLU A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
    Processing helix  chain 'C' and resid 2 through 13
    Processing helix  chain 'C' and resid 50 through 60
    Processing helix  chain 'C' and resid 68 through 75
    Processing helix  chain 'C' and resid 129 through 137
    Processing helix  chain 'C' and resid 207 through 216
    Processing helix  chain 'C' and resid 217 through 225
    Processing helix  chain 'C' and resid 231 through 236
      removed outlier: 3.587A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.599A  pdb=" N   GLU C 260 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 308
    Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27
      removed outlier: 6.685A  pdb=" N   VAL F  31 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 106 through 108
      removed outlier: 8.281A  pdb=" N   THR F  98 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE F  99 " --> pdb=" O   ALA F  80 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   ASP F 124 " --> pdb=" O   ALA F  81 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   LYS F 180 " --> pdb=" O   GLN F 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87
    Processing sheet with id=AA4, first strand: chain 'F' and resid 160 through 162
    Processing sheet with id=AA5, first strand: chain 'F' and resid 263 through 266
      removed outlier: 3.525A  pdb=" N   GLU F 266 " --> pdb=" O   PHE F 279 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ILE F 280 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   CYS F 290 " --> pdb=" O   ILE F 280 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASP F 282 " --> pdb=" O   SER F 288 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   SER F 288 " --> pdb=" O   ASP F 282 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 315 through 322
      removed outlier: 7.388A  pdb=" N   SER F 328 " --> pdb=" O   PRO F 343 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   MET F 330 " --> pdb=" O   PHE F 341 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   PHE F 341 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP F 332 " --> pdb=" O   GLU F 339 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.669A  pdb=" N   VAL D  31 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.121A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.121A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87
    Processing sheet with id=AB2, first strand: chain 'D' and resid 160 through 162
    Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 266
      removed outlier: 3.579A  pdb=" N   GLU D 266 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   ILE D 280 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   CYS D 290 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP D 282 " --> pdb=" O   SER D 288 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   SER D 288 " --> pdb=" O   ASP D 282 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 315 through 322
      removed outlier: 7.483A  pdb=" N   SER D 328 " --> pdb=" O   PRO D 343 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   MET D 330 " --> pdb=" O   PHE D 341 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   PHE D 341 " --> pdb=" O   MET D 330 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   TRP D 332 " --> pdb=" O   GLU D 339 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 27
      removed outlier: 6.668A  pdb=" N   VAL E  31 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.397A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 9.114A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LYS E 180 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AB8, first strand: chain 'E' and resid 98 through 99
      removed outlier: 8.157A  pdb=" N   THR E  98 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 162
    Processing sheet with id=AC1, first strand: chain 'E' and resid 264 through 266
      removed outlier: 4.873A  pdb=" N   ILE E 280 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   CYS E 290 " --> pdb=" O   ILE E 280 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 315 through 322
      removed outlier: 7.345A  pdb=" N   SER E 328 " --> pdb=" O   PRO E 343 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   MET E 330 " --> pdb=" O   PHE E 341 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE E 341 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   TRP E 332 " --> pdb=" O   GLU E 339 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 24 through 27
      removed outlier: 6.732A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.268A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   LYS B 180 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AC6, first strand: chain 'B' and resid 98 through 99
      removed outlier: 8.227A  pdb=" N   THR B  98 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AC8, first strand: chain 'B' and resid 264 through 266
      removed outlier: 3.583A  pdb=" N   GLU B 266 " --> pdb=" O   PHE B 279 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 275 through 277
    Processing sheet with id=AD1, first strand: chain 'B' and resid 315 through 322
      removed outlier: 7.221A  pdb=" N   SER B 328 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   MET B 330 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   PHE B 341 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP B 332 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 24 through 27
      removed outlier: 6.717A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.022A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.022A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   LYS A 180 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AD6, first strand: chain 'A' and resid 98 through 99
      removed outlier: 8.372A  pdb=" N   THR A  98 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AD8, first strand: chain 'A' and resid 264 through 266
      removed outlier: 4.997A  pdb=" N   ILE A 280 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   CYS A 290 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'A' and resid 316 through 322
      removed outlier: 3.515A  pdb=" N   TYR A 342 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 24 through 27
      removed outlier: 6.717A  pdb=" N   VAL C  31 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.156A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.156A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.699A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LYS C 180 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AE5, first strand: chain 'C' and resid 98 through 99
      removed outlier: 8.144A  pdb=" N   THR C  98 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE5
    Processing sheet with id=AE6, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AE7, first strand: chain 'C' and resid 264 through 266
      removed outlier: 3.529A  pdb=" N   GLU C 264 " --> pdb=" O   THR C 281 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   ILE C 280 " --> pdb=" O   CYS C 290 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   CYS C 290 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 322
      removed outlier: 3.603A  pdb=" N   THR C 340 " --> pdb=" O   TRP C 332 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   LYS C 334 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   VAL C 338 " --> pdb=" O   LYS C 334 " (cutoff:3.500A)

    621 hydrogen bonds defined for protein.
    1611 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 2.66

  Time building geometry restraints manager: 1.57 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 3000
        1.32 -     1.44: 4734
        1.44 -     1.57: 10038
        1.57 -     1.69: 91
        1.69 -     1.81: 90
  Bond restraints: 17953
  Sorted by residual:
  bond pdb=" CA  LYS C 149 "
       pdb=" C   LYS C 149 "
    ideal  model  delta    sigma   weight residual
    1.524  1.490  0.035 1.22e-02 6.72e+03 8.08e+00
  bond pdb=" C   THR D  98 "
       pdb=" O   THR D  98 "
    ideal  model  delta    sigma   weight residual
    1.235  1.201  0.034 1.26e-02 6.30e+03 7.49e+00
  bond pdb=" C   ILE D  99 "
       pdb=" O   ILE D  99 "
    ideal  model  delta    sigma   weight residual
    1.236  1.208  0.028 1.19e-02 7.06e+03 5.43e+00
  bond pdb=" CA  ILE D  99 "
       pdb=" CB  ILE D  99 "
    ideal  model  delta    sigma   weight residual
    1.540  1.511  0.029 1.36e-02 5.41e+03 4.60e+00
  bond pdb=" CA  VAL C 148 "
       pdb=" C   VAL C 148 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.027 1.28e-02 6.10e+03 4.52e+00
  ... (remaining 17948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 24228
        2.03 -     4.06: 310
        4.06 -     6.08: 24
        6.08 -     8.11: 11
        8.11 -    10.14: 4
  Bond angle restraints: 24577
  Sorted by residual:
  angle pdb=" N   LYS C 149 "
        pdb=" CA  LYS C 149 "
        pdb=" C   LYS C 149 "
      ideal   model   delta    sigma   weight residual
     108.96  116.67   -7.71 1.59e+00 3.96e-01 2.35e+01
  angle pdb=" C4'   A H   5 "
        pdb=" C3'   A H   5 "
        pdb=" O3'   A H   5 "
      ideal   model   delta    sigma   weight residual
     113.00  106.84    6.16 1.50e+00 4.44e-01 1.69e+01
  angle pdb=" N   LYS D  89 "
        pdb=" CA  LYS D  89 "
        pdb=" C   LYS D  89 "
      ideal   model   delta    sigma   weight residual
     113.20  108.24    4.96 1.21e+00 6.83e-01 1.68e+01
  angle pdb=" C   LYS D 344 "
        pdb=" N   LEU D 345 "
        pdb=" CA  LEU D 345 "
      ideal   model   delta    sigma   weight residual
     121.54  129.05   -7.51 1.91e+00 2.74e-01 1.55e+01
  angle pdb=" C   LYS C 344 "
        pdb=" N   LEU C 345 "
        pdb=" CA  LEU C 345 "
      ideal   model   delta    sigma   weight residual
     121.54  129.02   -7.48 1.91e+00 2.74e-01 1.53e+01
  ... (remaining 24572 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.33: 9344
       19.33 -    38.65: 1040
       38.65 -    57.98: 288
       57.98 -    77.30: 64
       77.30 -    96.63: 18
  Dihedral angle restraints: 10754
    sinusoidal: 4670
      harmonic: 6084
  Sorted by residual:
  dihedral pdb=" C3'   A H   6 "
           pdb=" C4'   A H   6 "
           pdb=" O4'   A H   6 "
           pdb=" C1'   A H   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      20.00   -7.86   27.86     1      8.00e+00 1.56e-02 1.74e+01
  dihedral pdb=" C4'   A H   6 "
           pdb=" O4'   A H   6 "
           pdb=" C1'   A H   6 "
           pdb=" C2'   A H   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00   29.45  -26.45     1      8.00e+00 1.56e-02 1.57e+01
  dihedral pdb=" CA  ASP D 106 "
           pdb=" C   ASP D 106 "
           pdb=" N   ILE D 107 "
           pdb=" CA  ILE D 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.31   19.69     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 10751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 2083
       0.043 -    0.087: 500
       0.087 -    0.130: 237
       0.130 -    0.173: 31
       0.173 -    0.217: 13
  Chirality restraints: 2864
  Sorted by residual:
  chirality pdb=" C3'   U G  17 "
            pdb=" C4'   U G  17 "
            pdb=" O3'   U G  17 "
            pdb=" C2'   U G  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.69    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" C3'   U G  15 "
            pdb=" C4'   U G  15 "
            pdb=" O3'   U G  15 "
            pdb=" C2'   U G  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C3'   U G  13 "
            pdb=" C4'   U G  13 "
            pdb=" O3'   U G  13 "
            pdb=" C2'   U G  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.67    0.20 2.00e-01 2.50e+01 9.54e-01
  ... (remaining 2861 not shown)

  Planarity restraints: 2998
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 203 "   -0.014 2.00e-02 2.50e+03   2.84e-02 8.06e+00
        pdb=" C   PHE B 203 "    0.049 2.00e-02 2.50e+03
        pdb=" O   PHE B 203 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS B 204 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 204 "    0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO C 205 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO C 205 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 205 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 226 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.88e+00
        pdb=" C   LYS E 226 "    0.038 2.00e-02 2.50e+03
        pdb=" O   LYS E 226 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU E 227 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2995 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1408
        2.74 -     3.28: 17142
        3.28 -     3.82: 30180
        3.82 -     4.36: 37190
        4.36 -     4.90: 62588
  Nonbonded interactions: 148508
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  45 "
            pdb=" OG1 THR A  47 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OD2 ASP D 212 "
            pdb=" OH  TYR D 225 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD2 ASP C 212 "
            pdb=" OH  TYR C 225 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   HIS A 242 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   SER F 197 "
            pdb=" OG  SER F 197 "
     model   vdw
     2.267 3.040
  ... (remaining 148503 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346))
  selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     19.070
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  17953  Z= 0.142
  Angle     :  0.562  10.139  24577  Z= 0.321
  Chirality :  0.048   0.217   2864
  Planarity :  0.004   0.057   2998
  Dihedral  : 17.652  96.628   6830
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 23.39 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.19), residues: 2094
  helix:  0.85 (0.24), residues: 528
  sheet:  0.35 (0.29), residues: 354
  loop :  0.20 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  61 
 TYR   0.012   0.001   TYR D 342 
 PHE   0.022   0.001   PHE B 203 
 TRP   0.004   0.000   TRP E 332 
 HIS   0.003   0.001   HIS E  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (17953)
  covalent geometry    : angle       0.56213 (24577)
  hydrogen bonds       : bond        0.20686 (  638)
  hydrogen bonds       : angle       8.38870 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 231
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
REVERT: F  113 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7165 (mp0)
REVERT: E  106 ASP cc_start: 0.7281 (m-30) cc_final: 0.6975 (p0)
REVERT: B  330 MET cc_start: 0.6707 (tpp) cc_final: 0.6213 (ttm)
REVERT: C  218 MET cc_start: 0.7052 (ttt) cc_final: 0.6759 (ttm)
  outliers start: 8
  outliers final: 1
  residues processed: 234
  average time/residue: 0.1310
  time to fit residues: 45.7698
Evaluate side-chains
  208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   96 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:    5.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 200 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.5980
   overall best weight:    1.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN
E 244 GLN
A  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.158430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.116790 restraints weight = 127824.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 6.98
r_work: 0.2793 rms_B_bonded: 6.33 restraints_weight: 2.0000
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  17953  Z= 0.259
  Angle     :  0.616  10.563  24577  Z= 0.321
  Chirality :  0.049   0.228   2864
  Planarity :  0.004   0.049   2998
  Dihedral  : 11.311  78.378   2866
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 22.80 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.19), residues: 2094
  helix:  0.41 (0.23), residues: 534
  sheet:  0.15 (0.29), residues: 360
  loop :  0.08 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  90 
 TYR   0.016   0.002   TYR A 225 
 PHE   0.016   0.002   PHE E   7 
 TRP   0.014   0.002   TRP A  86 
 HIS   0.004   0.001   HIS B  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 (17953)
  covalent geometry    : angle       0.61557 (24577)
  hydrogen bonds       : bond        0.04549 (  638)
  hydrogen bonds       : angle       5.92171 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 211
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  340 THR cc_start: 0.5599 (OUTLIER) cc_final: 0.4842 (p)
REVERT: E   99 ILE cc_start: 0.8653 (mt) cc_final: 0.8361 (mt)
REVERT: E  224 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7853 (ttp-170)
REVERT: E  227 LEU cc_start: 0.8748 (mm) cc_final: 0.8460 (mm)
REVERT: B  271 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8192 (ptm)
REVERT: B  296 ASP cc_start: 0.8958 (t0) cc_final: 0.8453 (t0)
REVERT: A  252 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8496 (mp)
REVERT: A  326 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (mt-10)
REVERT: A  333 CYS cc_start: 0.9126 (m) cc_final: 0.8670 (m)
REVERT: C  167 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8495 (pp)
REVERT: C  204 LYS cc_start: 0.8346 (mtpp) cc_final: 0.8110 (mmmt)
REVERT: C  226 LYS cc_start: 0.8602 (mmtm) cc_final: 0.7880 (ptmm)
REVERT: C  330 MET cc_start: 0.7293 (mmt) cc_final: 0.7057 (mmm)
  outliers start: 37
  outliers final: 17
  residues processed: 240
  average time/residue: 0.1206
  time to fit residues: 44.0737
Evaluate side-chains
  215 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 193
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  263 PHE
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  340 THR
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   36 ASP
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  326 GLU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue  167 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 174 optimal weight:    0.6980
   chunk 207 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 154 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 79 optimal weight:    0.4980
   chunk 127 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN
B  14 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.161594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.119835 restraints weight = 127386.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 6.94
r_work: 0.2838 rms_B_bonded: 6.35 restraints_weight: 2.0000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17953  Z= 0.135
  Angle     :  0.531  11.016  24577  Z= 0.272
  Chirality :  0.045   0.216   2864
  Planarity :  0.004   0.044   2998
  Dihedral  : 10.809  73.701   2864
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 23.44 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.19), residues: 2094
  helix:  0.54 (0.24), residues: 534
  sheet:  0.15 (0.29), residues: 360
  loop :  0.11 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  90 
 TYR   0.019   0.001   TYR D 278 
 PHE   0.015   0.001   PHE A 258 
 TRP   0.011   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (17953)
  covalent geometry    : angle       0.53137 (24577)
  hydrogen bonds       : bond        0.03597 (  638)
  hydrogen bonds       : angle       5.34612 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 223
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
REVERT: E  135 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7819 (mtt90)
REVERT: E  224 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7824 (ttp-170)
REVERT: E  227 LEU cc_start: 0.8691 (mm) cc_final: 0.8385 (mm)
REVERT: B  209 MET cc_start: 0.7937 (ttm) cc_final: 0.7542 (ttt)
REVERT: B  277 ASN cc_start: 0.8808 (m-40) cc_final: 0.8464 (m-40)
REVERT: B  296 ASP cc_start: 0.8725 (t0) cc_final: 0.8266 (t0)
REVERT: A  223 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8667 (pt0)
REVERT: A  333 CYS cc_start: 0.9053 (m) cc_final: 0.8660 (m)
REVERT: A  345 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6921 (tp)
REVERT: C  204 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8105 (mmmt)
REVERT: C  226 LYS cc_start: 0.8585 (mmtm) cc_final: 0.7909 (ptmm)
REVERT: C  330 MET cc_start: 0.7329 (mmt) cc_final: 0.7087 (mmm)
  outliers start: 35
  outliers final: 16
  residues processed: 248
  average time/residue: 0.1235
  time to fit residues: 46.5914
Evaluate side-chains
  216 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  132 ASP
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 179 optimal weight:    0.4980
   chunk 166 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 109 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0470
   chunk 101 optimal weight:    1.9990
   chunk 207 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9990
   overall best weight:    0.5078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.162736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.120551 restraints weight = 123248.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 6.84
r_work: 0.2863 rms_B_bonded: 6.33 restraints_weight: 2.0000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  17953  Z= 0.113
  Angle     :  0.506  11.336  24577  Z= 0.259
  Chirality :  0.045   0.416   2864
  Planarity :  0.003   0.041   2998
  Dihedral  : 10.390  75.308   2864
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 23.39 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.19), residues: 2094
  helix:  0.60 (0.24), residues: 540
  sheet:  0.21 (0.29), residues: 342
  loop :  0.21 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 135 
 TYR   0.014   0.001   TYR D 278 
 PHE   0.015   0.001   PHE A 258 
 TRP   0.009   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (17953)
  covalent geometry    : angle       0.50591 (24577)
  hydrogen bonds       : bond        0.03172 (  638)
  hydrogen bonds       : angle       5.03433 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 234
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.9073 (t) cc_final: 0.8767 (m)
REVERT: E   99 ILE cc_start: 0.8701 (mt) cc_final: 0.8485 (mt)
REVERT: E  106 ASP cc_start: 0.7955 (m-30) cc_final: 0.7586 (m-30)
REVERT: E  135 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7857 (mtt90)
REVERT: E  163 ASN cc_start: 0.8609 (t0) cc_final: 0.8209 (t0)
REVERT: E  224 ARG cc_start: 0.8095 (ttp-170) cc_final: 0.7742 (ttp-170)
REVERT: B  209 MET cc_start: 0.7908 (ttm) cc_final: 0.7571 (ttt)
REVERT: B  218 MET cc_start: 0.7193 (ttt) cc_final: 0.6951 (ttt)
REVERT: B  277 ASN cc_start: 0.8781 (m-40) cc_final: 0.8460 (m-40)
REVERT: B  284 GLN cc_start: 0.8307 (tp40) cc_final: 0.7736 (tt0)
REVERT: B  296 ASP cc_start: 0.8694 (t0) cc_final: 0.8270 (t0)
REVERT: A  223 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8613 (pt0)
REVERT: A  333 CYS cc_start: 0.9035 (m) cc_final: 0.8661 (m)
REVERT: A  345 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6822 (tp)
REVERT: C  167 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8302 (pp)
REVERT: C  204 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8200 (mmmt)
REVERT: C  226 LYS cc_start: 0.8568 (mmtm) cc_final: 0.7914 (ptmm)
REVERT: C  330 MET cc_start: 0.7380 (mmt) cc_final: 0.7119 (mmm)
  outliers start: 42
  outliers final: 25
  residues processed: 264
  average time/residue: 0.1343
  time to fit residues: 53.9120
Evaluate side-chains
  239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  281 THR
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  204 LYS
Chi-restraints excluded: chain C residue  321 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 102 optimal weight:    0.3980
   chunk 141 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 76 optimal weight:    2.9990
   chunk 133 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 107 optimal weight:    0.5980
   chunk 174 optimal weight:    1.9990
   chunk 185 optimal weight:    0.0670
   chunk 92 optimal weight:    0.1980
   overall best weight:    0.3518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 139 ASN
D 187 GLN
A  14 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.182963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.144917 restraints weight = 127085.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 5.96
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3621 r_free = 0.3621    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3621 r_free = 0.3621    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  17953  Z= 0.095
  Angle     :  0.489  10.600  24577  Z= 0.251
  Chirality :  0.044   0.395   2864
  Planarity :  0.003   0.041   2998
  Dihedral  : 10.127  75.867   2864
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 23.39 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.19), residues: 2094
  helix:  0.76 (0.24), residues: 540
  sheet:  0.38 (0.29), residues: 330
  loop :  0.31 (0.19), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 257 
 TYR   0.014   0.001   TYR D 278 
 PHE   0.016   0.001   PHE A 258 
 TRP   0.007   0.001   TRP D  86 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (17953)
  covalent geometry    : angle       0.48879 (24577)
  hydrogen bonds       : bond        0.02875 (  638)
  hydrogen bonds       : angle       4.80407 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 237
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: D  187 GLN cc_start: 0.8169 (mt0) cc_final: 0.7905 (mt0)
REVERT: D  264 GLU cc_start: 0.7574 (mp0) cc_final: 0.7211 (tt0)
REVERT: E  135 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7944 (mtt90)
REVERT: B  202 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7236 (tp30)
REVERT: B  218 MET cc_start: 0.7119 (ttt) cc_final: 0.6857 (ttt)
REVERT: B  284 GLN cc_start: 0.8236 (tp40) cc_final: 0.7726 (tt0)
REVERT: B  296 ASP cc_start: 0.7933 (t0) cc_final: 0.7660 (t0)
REVERT: C  167 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8247 (pp)
REVERT: C  226 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8196 (ptmm)
  outliers start: 37
  outliers final: 22
  residues processed: 263
  average time/residue: 0.1300
  time to fit residues: 51.8442
Evaluate side-chains
  241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  245 LEU
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  300 ASP
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  167 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 183 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 192 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 109 optimal weight:    0.7980
   chunk 104 optimal weight:    0.5980
   chunk 155 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 116 optimal weight:    0.0010
   overall best weight:    0.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
F  14 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.181593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.144110 restraints weight = 128490.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 5.76
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  17953  Z= 0.119
  Angle     :  0.511  11.245  24577  Z= 0.260
  Chirality :  0.045   0.410   2864
  Planarity :  0.003   0.038   2998
  Dihedral  : 10.043  75.382   2864
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 23.60 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.19), residues: 2094
  helix:  0.70 (0.24), residues: 540
  sheet:  0.29 (0.29), residues: 342
  loop :  0.22 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 126 
 TYR   0.014   0.001   TYR D 278 
 PHE   0.024   0.001   PHE A 258 
 TRP   0.007   0.001   TRP D  86 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (17953)
  covalent geometry    : angle       0.51070 (24577)
  hydrogen bonds       : bond        0.03019 (  638)
  hydrogen bonds       : angle       4.82365 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 220
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: D   96 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5928 (tt)
REVERT: D  264 GLU cc_start: 0.7675 (mp0) cc_final: 0.7364 (tt0)
REVERT: E  135 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7879 (mtt90)
REVERT: B  202 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7243 (tp30)
REVERT: B  218 MET cc_start: 0.7147 (ttt) cc_final: 0.6898 (ttt)
REVERT: B  284 GLN cc_start: 0.8203 (tp40) cc_final: 0.7726 (tt0)
REVERT: B  296 ASP cc_start: 0.8005 (t0) cc_final: 0.7738 (t0)
REVERT: C  167 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8302 (pp)
  outliers start: 32
  outliers final: 25
  residues processed: 244
  average time/residue: 0.1332
  time to fit residues: 49.7750
Evaluate side-chains
  235 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 207
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  209 MET
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  167 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 188 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 146 optimal weight:    0.0060
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 159 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 173 optimal weight:    0.5980
   chunk 189 optimal weight:    0.7980
   overall best weight:    0.3996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 139 ASN
E 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.183219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.145092 restraints weight = 128602.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 6.09
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  17953  Z= 0.100
  Angle     :  0.497  10.559  24577  Z= 0.253
  Chirality :  0.044   0.416   2864
  Planarity :  0.003   0.036   2998
  Dihedral  :  9.949  73.998   2864
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 24.03 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.19), residues: 2094
  helix:  0.70 (0.24), residues: 540
  sheet:  0.45 (0.29), residues: 330
  loop :  0.29 (0.18), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 126 
 TYR   0.013   0.001   TYR D 278 
 PHE   0.021   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (17953)
  covalent geometry    : angle       0.49661 (24577)
  hydrogen bonds       : bond        0.02825 (  638)
  hydrogen bonds       : angle       4.72797 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 216
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: D  264 GLU cc_start: 0.7601 (mp0) cc_final: 0.7290 (tt0)
REVERT: E  135 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7877 (mtt90)
REVERT: B  202 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7209 (tp30)
REVERT: B  218 MET cc_start: 0.7151 (ttt) cc_final: 0.6925 (ttt)
REVERT: B  284 GLN cc_start: 0.8171 (tp40) cc_final: 0.7695 (tt0)
REVERT: B  296 ASP cc_start: 0.7952 (t0) cc_final: 0.7670 (t0)
REVERT: C  167 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8266 (pp)
REVERT: C  330 MET cc_start: 0.6950 (mmm) cc_final: 0.6650 (mmt)
  outliers start: 29
  outliers final: 24
  residues processed: 236
  average time/residue: 0.1219
  time to fit residues: 43.9982
Evaluate side-chains
  231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 205
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   51 VAL
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  167 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 135 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 189 optimal weight:    1.9990
   chunk 114 optimal weight:    0.3980
   chunk 53 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 174 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 188 optimal weight:    0.0670
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5318

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.181819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.143434 restraints weight = 128535.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 6.01
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17953  Z= 0.113
  Angle     :  0.506  10.682  24577  Z= 0.255
  Chirality :  0.045   0.433   2864
  Planarity :  0.003   0.036   2998
  Dihedral  :  9.916  73.959   2864
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 23.82 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.19), residues: 2094
  helix:  0.69 (0.24), residues: 540
  sheet:  0.46 (0.29), residues: 330
  loop :  0.27 (0.18), residues: 1224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 257 
 TYR   0.013   0.001   TYR D 278 
 PHE   0.015   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A  86 
 HIS   0.004   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (17953)
  covalent geometry    : angle       0.50571 (24577)
  hydrogen bonds       : bond        0.02904 (  638)
  hydrogen bonds       : angle       4.76059 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 206
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
REVERT: D  264 GLU cc_start: 0.7567 (mp0) cc_final: 0.7269 (tt0)
REVERT: E  135 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7888 (mtt90)
REVERT: B  202 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7238 (tp30)
REVERT: B  218 MET cc_start: 0.7216 (ttt) cc_final: 0.7005 (ttt)
REVERT: B  284 GLN cc_start: 0.8216 (tp40) cc_final: 0.7735 (tt0)
REVERT: B  296 ASP cc_start: 0.8033 (t0) cc_final: 0.7732 (t0)
REVERT: C  167 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8296 (pp)
REVERT: C  226 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8086 (mtmm)
  outliers start: 32
  outliers final: 26
  residues processed: 228
  average time/residue: 0.1331
  time to fit residues: 46.5556
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 200
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  167 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 156 optimal weight:    0.9980
   chunk 91 optimal weight:    0.4980
   chunk 183 optimal weight:    0.6980
   chunk 184 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 87 optimal weight:    0.7980
   chunk 168 optimal weight:    0.8980
   chunk 203 optimal weight:    0.0570
   overall best weight:    0.5098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.182052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.143598 restraints weight = 124850.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 5.95
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17953  Z= 0.110
  Angle     :  0.509  12.379  24577  Z= 0.256
  Chirality :  0.044   0.420   2864
  Planarity :  0.003   0.036   2998
  Dihedral  :  9.880  73.464   2864
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 23.82 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.19), residues: 2094
  helix:  0.68 (0.24), residues: 540
  sheet:  0.58 (0.28), residues: 342
  loop :  0.20 (0.19), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 138 
 TYR   0.012   0.001   TYR D 278 
 PHE   0.016   0.001   PHE A 258 
 TRP   0.008   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (17953)
  covalent geometry    : angle       0.50929 (24577)
  hydrogen bonds       : bond        0.02879 (  638)
  hydrogen bonds       : angle       4.72882 ( 1699)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: D  264 GLU cc_start: 0.7553 (mp0) cc_final: 0.7321 (tt0)
REVERT: E  135 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7895 (mtt90)
REVERT: B  202 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7230 (tp30)
REVERT: B  218 MET cc_start: 0.7177 (ttt) cc_final: 0.6955 (ttt)
REVERT: B  284 GLN cc_start: 0.8266 (tp40) cc_final: 0.7769 (tt0)
REVERT: B  296 ASP cc_start: 0.7990 (t0) cc_final: 0.7708 (t0)
REVERT: C  167 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8295 (pp)
REVERT: C  226 LYS cc_start: 0.8586 (ptmm) cc_final: 0.8113 (mtmm)
REVERT: C  330 MET cc_start: 0.6913 (mmm) cc_final: 0.6421 (mmm)
  outliers start: 31
  outliers final: 27
  residues processed: 224
  average time/residue: 0.1353
  time to fit residues: 45.8430
Evaluate side-chains
  231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 202
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  252 ILE
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  167 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 54 optimal weight:    2.9990
   chunk 134 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 188 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 114 optimal weight:    0.0060
   chunk 193 optimal weight:    3.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.181875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143537 restraints weight = 130572.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 6.09
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17953  Z= 0.117
  Angle     :  0.511  11.938  24577  Z= 0.257
  Chirality :  0.045   0.433   2864
  Planarity :  0.003   0.034   2998
  Dihedral  :  9.875  73.473   2864
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 23.66 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.19), residues: 2094
  helix:  0.63 (0.24), residues: 540
  sheet:  0.36 (0.29), residues: 342
  loop :  0.20 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 138 
 TYR   0.012   0.001   TYR D 278 
 PHE   0.016   0.001   PHE A 258 
 TRP   0.008   0.001   TRP A  86 
 HIS   0.003   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (17953)
  covalent geometry    : angle       0.51127 (24577)
  hydrogen bonds       : bond        0.02933 (  638)
  hydrogen bonds       : angle       4.76123 ( 1699)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 211
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: D   33 THR cc_start: 0.8656 (t) cc_final: 0.8206 (m)
REVERT: D  264 GLU cc_start: 0.7576 (mp0) cc_final: 0.7322 (tt0)
REVERT: E  135 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7898 (mtt90)
REVERT: B  202 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7241 (tp30)
REVERT: B  218 MET cc_start: 0.7203 (ttt) cc_final: 0.6995 (ttt)
REVERT: B  284 GLN cc_start: 0.8288 (tp40) cc_final: 0.7784 (tt0)
REVERT: B  296 ASP cc_start: 0.8046 (t0) cc_final: 0.7773 (t0)
REVERT: A  136 ASN cc_start: 0.8822 (m-40) cc_final: 0.8587 (m-40)
REVERT: C  167 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8298 (pp)
REVERT: C  226 LYS cc_start: 0.8578 (ptmm) cc_final: 0.8119 (mtmm)
REVERT: C  330 MET cc_start: 0.7070 (mmm) cc_final: 0.6608 (mmm)
  outliers start: 32
  outliers final: 26
  residues processed: 233
  average time/residue: 0.1369
  time to fit residues: 48.6462
Evaluate side-chains
  234 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 206
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  131 VAL
Chi-restraints excluded: chain F residue  288 SER
Chi-restraints excluded: chain F residue  321 THR
Chi-restraints excluded: chain D residue   78 ASP
Chi-restraints excluded: chain D residue  103 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  197 SER
Chi-restraints excluded: chain E residue   51 VAL
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  320 VAL
Chi-restraints excluded: chain B residue  132 ASP
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  167 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 208
   random chunks:
   chunk 154 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 148 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E 163 ASN
C 175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.179688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.140782 restraints weight = 130592.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 6.04
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3575
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3575 r_free = 0.3575    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3575 r_free = 0.3575    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3575
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  17953  Z= 0.151
  Angle     :  0.541  11.682  24577  Z= 0.272
  Chirality :  0.046   0.437   2864
  Planarity :  0.003   0.034   2998
  Dihedral  :  9.930  73.734   2864
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 23.82 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.19), residues: 2094
  helix:  0.55 (0.24), residues: 540
  sheet:  0.34 (0.29), residues: 342
  loop :  0.15 (0.18), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 138 
 TYR   0.013   0.001   TYR D 278 
 PHE   0.016   0.001   PHE A 258 
 TRP   0.008   0.001   TRP A  86 
 HIS   0.003   0.001   HIS D 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (17953)
  covalent geometry    : angle       0.54137 (24577)
  hydrogen bonds       : bond        0.03186 (  638)
  hydrogen bonds       : angle       4.89954 ( 1699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3375.68 seconds
wall clock time: 59 minutes 4.53 seconds (3544.53 seconds total)